Nucleotide Sequence Differences Research Articles

Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences

The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max) in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp) was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence similarity among subgroups IA, IB and IC ranged from 84.3 to 89% in ITS1 and from 93.3 to 95.6% in ITS2. Nucleotide sequence similarity of 99.1% and 99.3-100% for ITS1 and ITS2, respectively, was observed between AG-4 soybean isolates causing hypocotyl rots and the AG-4 HGI tester. The similarity of the nucleotide sequence of the ITS-5.8S rDNA region confirmed that the R. solani Brazilian isolates causing foliar blight are AG-1 IA and isolates causing hypocotyl rot symptoms are AG-4 HGI. The ITS-5.8S rDNA sequence was not determinant for the identification of the AG-2-2 IIIB R. solani soybean isolate.

Large‐scale genetic differentiation of Pagrus pagrus in the Atlantic

Red porgy Pagrus pagrus from the north‐eastern, north‐western and south‐western Atlantic were found to be genetically distinct as determined by mitochondrial DNA analysis. There were no shared composite restriction fragment haplotypes, and nucleotide sequence differences averaged 2% among these locations.

Development of Internal Transcribed Spacer Regions Amplification Restriction Fragment Length Polymorphism Method and Its Application in Monitoring the Population of Zygosaccharomyces rouxii M2 in Miso Fermentation

Recently, the use of the dry yeast of Zygosaccharomyces rouxii M2 for miso (soybean paste) fermentation has been established. A molecular monitoring method was developed and validated in this study to analyze the population of Z. rouxii M2 during the fermentation. The method was based on the restriction patterns of internal transcribed spacer (ITS) regions of the rDNA using Hae III and Hha I. Among the homologous ITS regions of Z. rouxii strains, Z. rouxii M2 produced diagnostic bands by which it can be differentiated from the other strains used. The specific restriction bands were due to the difference in nucleotide sequence of two different copies of ITS of Z. rouxii M2. Both ITS copies showed 94% sequence similarity but a 13-bp nucleotide substitution and a 19-bp deletion were found in the ITS1 region. Phylogenetic trees were constructed based on ITS and 18S rDNA sequences and it was found that the ITS sequences provide better resolution for the classification of Z. rouxii M2. Since Z. rouxii M2 is a promising strain for use in miso fermentation as a dry starter, the method developed is significant in terms of industrial application in monitoring the growth of Z. rouxii M2 in miso fermentation.

Characterization of the DNA nucleotide sequences in the genome of red sea bream iridoviruses isolated in Korea

Abstract The nucleotide sequences of DNA fragments amplified by polymerase chain reaction (PCR) from four different genomic regions of nine red sea bream iridoviruses (RSIVs) isolated from different species of fish, different areas and in different years in Korea were compared with the reported reference sequences. One isolate, RSIV Namhae, showed 100% homology to the reference sequences, while the other eight isolates, which appeared to contain identical nucleotide sequences, showed 96.6–98.9% homology with reference sequences depending upon the target regions of PCR gene amplification. However, differences in nucleotide sequences were not apparent between the RSIVs isolated in different locations, in different years or in different host species. We also cloned and sequenced the 3′ end flanking region (K1) of the DNA polymerase (DPOL) gene using the cassette ligation-mediated PCR method. This sequence was 4436-bp long and possessed two open reading frames (ORF-1 and ORF-2) oriented in opposite directions. The putative proteins encoded by these two ORFs could not be characterized by comparison with the proteins of other species in the data banks. The presence of the ribonucleotide reductase small subunit (RNRS) gene at the 3′ end of the K1 region allowed us to determine that these two genes, RNRS and DPOL, are separated 5508 bp and oriented in the same direction in the genome of RSIV. Moreover, it is of interest that a Pst I-restriction fragment, of which the sequence but not the location within the RSIV genome had previously been reported, is located at nucleotide positions from 1096 to 2054, extending from within the ORF-1 region, spanning the intervening sequence between ORF-1 and ORF-2, and extending into the ORF-2 region. Various repeating sequences up to 86 bp were present at the 3′ ends of ORFs, especially within the nucleotide sequences at the 3′ terminus of ORF-2. No similarities were detected when the DNA sequences of the K1 region were compared to the DNA sequences of a repetitive element in the genome of other iridoviruses.

Single-strand conformation polymorphism (SSCP) assays for major histocompatibility complex B genotyping in chickens

We have developed a DNA-based method for defining MHC B system genotypes in chickens. Genotyping by this method requires neither prior determination of allele-specific differences in nucleotide sequence nor the preparation of haplotype-specific alloantisera. Allelic differences at chicken B-F (class I) and B-L (class II) loci are detected in PCR single-strand conformation polymorphism (SSCP) assays. PCR primer pairs were designed to hybridize specifically with conserved sequences surrounding hypervariable regions within the two class I and two class I loci of the B-complex and used to generate DNA fragments that are heat- and formamide-denatured and then analyzed on nondenaturing polyacrylamide gels. PCR primer pairs were tested for the capacity to produce SSCP patterns allowing the seven B haplotypes in the MHC B congenic lines, and seven B haplotypes known to be segregating in two commercial broiler breeder lines to be distinguished. Primer pairs were further evaluated for their capacity to reveal the segregation of B haplotypes in a fully pedigreed family and in a closed population. Concordance was found between SSCP patterns and previously assigned MHC types. B-F and B-L SSCP patterns segregated in linkage as expected for these closely linked loci. We conclude that this method is valuable for defining MHC B haplotypes and for detecting potential recombinant haplotypes especially when used in combination with B-G (class IV) typing by restriction fragment pattern.

Assessment of hemagglutinin sequence heterogeneity during influenza virus transmission in families.

To examine the molecular epidemiology of influenza virus transmission, the nucleotide sequences of the HA1 domain of the hemagglutinin (HA) gene of 57 influenza A and 24 influenza B viruses recovered in a single season were analyzed. No nucleotide sequence differences were found among the 10 viruses that were recovered twice from the same patient. The nucleotide sequences of influenza A viruses were identical within each family but varied among the 14 families included in the study. The sequences of influenza A viruses recovered from 18 residents of the same community showed that 83% of the viruses differed from the others by at least 1 nucleotide residue. These findings indicate that most cases of influenza in households in which 1 family member has been infected are the result of secondary transmission from the index patient and not of acquisition from other community sources. Substantial genetic conservation during virus transmission within households is indicated.

Potato spindle tuber viroid strains of different pathogenicity induces and suppresses expression of common and unique genes in infected tomato.

Viroids are the smallest plant pathogens. These RNAs do not encode proteins and are not encapsidated, and yet they can replicate autonomously, move systemically, and cause diseases in infected plants. Notably, strains of a viroid with subtle differences in nucleotide sequences can cause dramatically different symptoms in infected plants. These features make viroids unique probes to investigate the role of a pathogenic RNA genome in triggering host responses. We conducted a comprehensive analysis of the differential gene expression patterns of tomato plants at various stages of infection by a mild and severe strain of Potato spindle tuber viroid (PSTVd). We also compared tomato gene expression altered by the PSTVd strains with that altered by Tobacco mosaic virus (TMV). Our analyses revealed that the two PSTVd strains altered expression of both common and unique tomato genes. These genes encode products involved in defense/stress response, cell wall structure, chloroplast function, protein metabolism, and other diverse functions. Five genes have unknown functions. Four genes are novel. The expression of some but not all of these genes was also altered by TMV infection. Our results indicate that viroids, although structurally simple, can trigger complex host responses. Further characterization of viroid-altered gene expression in a host plant should help understand viroid pathogenicity and, potentially, the mechanisms of RNA-mediated regulation of plant gene expression.

FlaA-like sequences containing internal termination codons (TAG) in urease-positive thermophilic Campylobacter isolated in Japan.

To demonstrate two flaA-like sequences containing two internal termination codons (TAG) in two Japanese strains of urease-positive thermophilic Campylobacter (UPTC). A primer pair of A1 and A2, which ought to generate a product of approx. 1700 bp of the flaA gene for Campylobacter jejuni, was used to amplify products of approx. 1450 bp for two Japanese strains of UPTC, CF89-12 and CF89-14. After molecular cloning and sequencing, the nucleotide sequences of the amplicons from the two strains were found to be 1461 bp in length and to have nucleotide sequence differences in relation to each other at four nucleotide positions, respectively. Nucleotide and amino acid sequence alignment and homology analysis demonstrated that the polymerase chain reaction (PCR) amplicons from the two Japanese strains have approx. 83% nucleotide and 80% amino acid sequence homology to the possible open reading frame of the flaA gene of UPTC NCTC 12892. Surprisingly, both PCR amplicons from the Japanese UPTC have two internal termination codons (TAG) at nucleotide positions from 775 to 777 and 817 to 819, respectively.

Development and Characterization of Microsatellite and RFLP‐Derived PCR Markers in Oat

Two sources were evaluated for the production of polymerase chain reaction (PCR) markers for oat (Avena spp.). First, nucleotide sequences were determined for 250 unique clones from oat microsatellite‐enriched genomic libraries. Forty‐four of the 63 primer pairs designed were functional, of which 18 (41%) were polymorphic among 13 Avena species and six (14%) were polymorphic between oat cultivars Kanota and Ogle. Second, primers were designed from the sequences of six cDNA fragment length polymorphism (RFLP) probes. Primer pairs from all six cDNA clones were polymorphic among the 13 Avena species, three were polymorphic between Kanota and Ogle, but only one was polymorphic directly between ‘Clintland 64’ and IL86‐5698. However, by cloning and sequencing the PCR products from Clintland 64 and IL86‐5698, it was possible to identify nucleotide sequence differences at restriction enzyme cutting sites in DNA fragments from two other primer pairs. Using the two types of markers, we placed nine loci on the hexaploid oat restriction RFLP map. The RFLP‐derived markers often mapped to the same or similar positions as the corresponding RFLP markers within and between mapping populations. The sequence analysis also revealed single nucleotide polymorphisms (SNPs) not at restriction enzyme cutting sites. Since multiple SNPs could be detected even within genes and the techniques for the development of SNPs and microsatellites are similar, it may be possible to identify more informative SNP markers than microsatellites from the same type of analysis.

分子疫学的手法に基づいた食中毒の監視体制; パルスネットの構築

As the foods are stocked below freezing and widely distributed, a kind of food-borne outbreak which occurs in separate regions or in different time, so called "diffuse outbreak", has been found at the present day. Unless the outbreak is early recognized, the number of victims would increase. Some methods have been developed to analyze the relatedness of bacteria isolated from the patients of enteric infections. PFGE, pulsed-field gel electrophoresis, is one of the methods and powerful to discriminate the difference in nucleotide sequences among bacterial genomes. Availability of PFGE analysis is appreciated to examine the linkage of each incident of food-borne infections in epidemiological investigation. A PFGE network, PulseNet Japan, is now under construction among National Institute of Infectious Diseases, local Health Institutes and Ministry of Health, Labour and Welfare.

Proviral genomic sequence analysis of Chinese donkey leukocyte attenuated equine infectious anemia virus vaccine and its parental virus strain Liaoning

Proviral DNA was extracted from donkey leukocyte infected with Chinese donkey leukocyte attenuated equine infectious anemia virus (DLA-EIAV), and peripheral blood lymphocytes (PBL) from a horse infected with the virulent EIAV strain Liaoning (EIAV L). The entire proviral DNA from both viruses was cloned and sequenced. The lengths of complete genomic sequences of DLA-EIAV and EIAV L provirus were 8266 bp and 8235 bp, respectively. Sequence comparison indicated that DLA-EIAV shares 97.0% and 97.5% in sequence homology with EIAV L and donkey-adapted EIAV (DA-EIAV), respectively. Lots of variations occurred in long terminal repeat (LTR, consisting of U3, R, U5), ORF S2, and env regions between DLA-EIAV and EIAV L. The nucleotide sequence differences of the two viruses in U3, R, U5, ORF S2, and env are 13.2%, 7.5%, 5.1%, 3.9%, and 2.7%, respectively, and predicted amino acid sequence differences in env and S2 coding regions are 4.4% and 8.8%, respectively. Six conserved regions are characterized in Gp90. There is a cis-activating GATA motif in ENH of DLA-EIAV and EIAV L. Two N-linked glycosylation sites disappeared in DLA-EIAV Gp90 in comparison with that of EIAV L. A bHLH transcription factor binding consensus sequence was found in LTR of DLA-EIAV but not in EIAV L. Furthermore, there is a mutation in the stem of DLA-EIAV TAR resulting in formation of a uridine tuber. Further study is needed to uncover the relationship between sequence changes and their biological functions of DLA-EIAV and L.

Absence of ras gene mutations in UV-induced malignant melanomas correlates with a dermal origin of melanocytes in Monodelphis domestica

The South American opossum, Monodelphis domestica, has been used as a model system to study ultraviolet (UV)-induced genetic alterations that lead to the development of melanoma. Suckling young of Monodelphis exposed to multiple doses of UVB radiation can develop benign or malignant melanomas later as adults. Point mutations predominantly at codon 61 of the N-ras gene have been found in melanomas from sun-exposed body sites in humans. To determine if similar mutations are associated with UV-induced melanoma in Monodelphis, the nucleotide sequence of a Monodelphis N-ras cDNA was determined, and the occurrence of ras mutations in melanomas from UV-irradiated opossums was investigated. Single-strand conformation polymorphism analysis revealed no mutations in either the Monodelphis N-ras or H-ras genes in any of 24 primary malignant melanoma samples analyzed in this study. The disparate association of ras mutations with melanoma in humans and Monodelphis may be explained by differences in nucleotide sequence at codon 61 of the N-ras gene as well as differences in skin architecture between the two species. These results support the contention that a mutationally activated N-ras gene contributes to the vertical growth phase, which is specific to the progression of malignant melanoma in humans.

The absence of disease-specific polymorphisms within the HLA-B51 gene that is the susceptible locus for Behçet's disease.

Behçet's disease is known to be associated with HLA-B51 in many different populations. Genetic evidence supports that the susceptible gene for Behçet's disease is the HLA-B51 allele at the HLA-B locus. This study was aimed to determine the HLA-B51 nucleotide sequence variation in three Behçet's disease patients and three healthy controls in order to elucidate if any disease specific mutations or polymorphisms may exist in the HLA-B51 gene of patients. Long-range polymerase chain reaction (PCR) was first carried out to give a PCR-amplified product of 9.5 kb which was then used as a template for nested PCR to give a final amplified product of 4.2 kb. This final product containing the 1.3-kb promoter/enhancer region and the entire HLA-B gene except for a 363-bp 3' terminal end segment encoding the 3' untranslated region was subcloned by the BP cloning technique and sequenced. The sequencing results showed that all the patients possessed the HLA-B*51011 allele, and there were no differences in the exonic nucleotide sequences between the three Behçet's disease patients and the three healthy controls. The HLA-B*51011 intronic and promoter/enhancer nucleotide sequences from the three patients had 22 single nucleotide polymorphisms (SNPs), a single insertion of 6 bp and a single deletion of 2 bp. On the other hand, the three healthy controls had 24 SNPs in their intronic and promoter/enhancer regions. However, none of these polymorphisms in the patients were specific for the disease. Therefore, these results clearly demonstrate that the HLA-B exonic sequence that encodes the HLA-B51 allele is the real pathogenic factor in Behçet's disease.

PHYLOGENETIC RELATIONSHIPS OF SPECIES OF RAYMUNIDA (DECAPODA: GALATHEIDAE) BASED ON MORPHOLOGY AND MITOCHONDRIAL CYTOCHROME OXIDASE SEQUENCES, WITH THE RECOGNITION OF FOUR NEW SPECIES

Abstract The species of the genus Raymunida from the Pacific and Indian oceans are revised using morphological characters and the mitochondrial cytochrome oxidase subunit I sequences. Four new species are described (R. confundens, R. dextralis, R. erythrina, and R. insulata), and the status of R. bellior and R. elegantissima are revised. The species of Raymunida can be identified by subtle morphological characters, which match differences in mitochondrial nucleotide sequences. Therefore, the sequence divergences confirm the specific and phylogenetic value of some morphological characters (e.g., length of the mesial spine on the basal antennal segment, length of the walking legs). Furthermore, they confirm the importance of the color pattern as a diagnostic character. The widespread species (R. elegantissima), known from the Philippines to Fiji, shows minimal divergence between specimens from different localities (maximum of 3 nucleotide differences or 0.2% mean divergence). The phylogenetic reconstruction...

Structural analysis of cDNA encoding thymidylate synthase in hepatic metastases of human colorectal tumors.

The enzyme thymidylate synthase (TS) is an important target of 5-fluorouracil (FUra) that is utilized for the treatment of disseminated colorectal cancer. One determinant of clinical response to FUra-based therapy is TS expression. with high levels of expression being predictive of poor response. In the present investigation the levels of immunoreactive TS were analyzed in human colon metastases in the liver (n=l1). The levels of TS ranged from 0.30 to 4.60 pmol TS/g tissue. A good correlation was observed between the levels of immunoreactive TS and TS mRNA (n=6, r=0.69). Of the 11 metastases analyzed, 5 exhibited relatively high levels of TS expression. Two metastases with high TS expression were obtained from patients who received adjuvant therapy with FUra. In 4 metastases with relatively high levels of TS expression, TS gene copy number was analyzed. No evidence for amplification of TS gene sequences was observed. The basis for the high levels of TS expression was examined by structural analysis of TS cDNA. No nucleotide sequence differences were detected in the coding regions of the TS genes from the metastases. Mutations were detected at positions 961 and/or 1031 in the 3'-untranslated regions of the TS gene from the metastases; mutations at these sites were also detected in DNA isolated from normal colon mucosa (n=4) and primary colorectal tumors (n=4). No correlation was observed between TS expression and the nucleotide alterations at these positions. Polymorphism was observed in the 5'-untranslated regions of the TS gene in hepatic metastases (n=6). A general trend was observed between the structure of the 5'-untranslated region of the gene and TS expression.

Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification

Restriction analysis detected two types of bigeye tuna (α and β); the α type was in the majority in the Atlantic but nearly absent in the Indo‐Pacific. The β type shared a larger number of restriction sites with other species than the conspecific β type, but bigeye‐specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub‐species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas.

Nucleotide sequence differences reveal genetic variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail host of schistosomiasis in the lower Mekong Basin

To investigate the phylogenetic relationships among the different strains of the polytypic snailNeotricula aperta , mitochondrial-DNA sequence data were sampled from six populations from central and southern Laos, eastern Cambodia, and northeast Thailand. Part of the cytochrome c oxidase subunit I gene was sequenced for 21 individuals from 7 populations, with a 598 bp sequence used in the analyses. Evolutionary distances were estimated as the Kimura two-parameter distance ×100 (D). The samples were taken from the Mekong, Mul and Xé Bang-Fai rivers of the lower Mekong Basin. The snail Tricula bollingi was used as an outgroup. The least amount of genetic divergence was found where the Thai γ-strain was compared with the other N. aperta samples (D, 1.6–6.4), and next for the Xé Bang-Fai river γ-strain sample when compared with the other N. aperta (D, 2.8–7.5). Large distances were apparent between the β-strain and all the γ-strain populations (D, 4.7–8.3). The γ-strain population of northeast Thailand comprised two cryptic taxa which were relatively well diverged (D=2.1). The findings agreed with those of earlier studies based on rRNA gene RFLP variation. The findings were consistent with earlier evidence suggesting dispersal of snails from highland streams in central Laos (e.g. Xé Bang-Fai) into the Mekong river of northeast Thailand; this is proposed as an explanation for the cryptic taxa in the region. The γ-strain of Cambodia and southern Laos has been shown to act as intermediate host for Schistosoma mekongi. Such findings are important in the limitation of Mekong schistosomiasis as they relate to the timing and location of snail control measures. A revised phylogeography is presented for the Triculinae on the basis of the present findings and current palaeoÍgeographic models for Southeast Asia.

Nucleotide sequence differences reveal genetic variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail host of schistosomiasis in the lower Mekong Basin

To investigate the phylogenetic relationships among the different strains of the polytypic snailNeotricula aperta , mitochondrial-DNA sequence data were sampled from six populations from central and southern Laos, eastern Cambodia, and northeast Thailand. Part of the cytochrome c oxidase subunit I gene was sequenced for 21 individuals from 7 populations, with a 598 bp sequence used in the analyses. Evolutionary distances were estimated as the Kimura two-parameter distance ×100 (D). The samples were taken from the Mekong, Mul and Xe Bang-Fai rivers of the lower Mekong Basin. The snail Tricula bollingi was used as an outgroup. The least amount of genetic divergence was found where the Thai γ-strain was compared with the other N. aperta samples (D, 1.6–6.4), and next for the Xe Bang-Fai river γ-strain sample when compared with the other N. aperta (D, 2.8–7.5). Large distances were apparent between the β-strain and all the γ-strain populations (D, 4.7–8.3). The γ-strain population of northeast Thailand comprised two cryptic taxa which were relatively well diverged (D=2.1). The findings agreed with those of earlier studies based on rRNA gene RFLP variation. The findings were consistent with earlier evidence suggesting dispersal of snails from highland streams in central Laos (e.g. Xe Bang-Fai) into the Mekong river of northeast Thailand; this is proposed as an explanation for the cryptic taxa in the region. The γ-strain of Cambodia and southern Laos has been shown to act as intermediate host for Schistosoma mekongi. Such findings are important in the limitation of Mekong schistosomiasis as they relate to the timing and location of snail control measures. A revised phylogeography is presented for the Triculinae on the basis of the present findings and current palaeoIgeographic models for Southeast Asia.

Listeria monocytogenes Lineage Group Classification by MAMA-PCR of the Listeriolysin Gene

Nucleotide sequence differences within several virulence genes, including the listeriolysin O (hly) gene, are associated with three evolutionary lineage groups of Listeria monocytogenes. Because the ability of L. monocytogenes to cause disease may vary by evolutionary lineage group, rapid discrimination among the three lineage types may be important for estimating pathogenic potential. A Mismatch Amplification Mutation Assay (MAMA) was developed and used to rapidly screen and characterize L. monocytogenes isolates with regard to lineage type. A standard PCR amplified a 446-bp region within the hly gene with all three L. monocytogenes lineage genotypes. MAMA primers to four different sites within this region of the hly gene were designed to amplify under the same PCR conditions and generated amplicons, the size of which depended on the isolate genotype. Ninety-seven L. monocytogenes isolates were screened. All isolates, except ATCC 19116, could be classified by MAMA PCR as one of the three hly genotypes. Overall, 56, 36, and 4 of the 97 isolates tested were type 1, 2, or 3 respectively. Among the 26 patient isolates, 85%, 15%, and 0% were type 1, 2, or 3 respectively; for the 60 food isolates, 54% were type 1, 43% were type 2, and 3% were type 3. The combination of these MAMA PCR analyses provides a rapid method to screen and categorize L. monocytogenes isolates because of conserved nucleotide differences within the hly gene.

Phylogeny of Thogoto virus.

Thogoto virus is a tick-borne member of the family Orthomyxoviridae. Previously, based on the similarity in antigenic relationship by cross-neutralization test, all virus strains were concluded to have derived from the same origin. In this study, we obtained partial gene sequences of 4 genes (PB1-like protein, PA-like protein, glycoprotein, and nucleoprotein) of 8 Thogoto virus strains isolated in Africa, Asia, and Europe and studied the genetic variation and phylogeny. Unrooted phylogenetic trees created by both neighbor-joining and maximum likelihood methods based on nucleotide and amino acid sequences for 4 genes were mostly similar and revealed two lineages, Euro-Asian and African. Intra-lineage nucleotide sequence variation was greater in the Euro-Asian lineage than in the African lineage for all 4 genes. Furthermore, for the strains of Euro-Asian lineage, variations for two genes associated with RNA-dependent RNA polymerase activities were greater than those for glycoprotein or nucleoprotein gene, based on both nucleotide and amino acid sequence differences as well as on synonymous and nonsynonymous differences, indicating greater mutation rates for the polymerase activity genes in these strains.